Paper Title: Cross-species single cell atlas of mammalian brain evolution
This repository contains the analysis code and scripts for the study "Cross-species single cell atlas of mammalian brain evolution". We integrated single-cell transcriptomic data across multiple mammalian species to construct a comprehensive cell-type atlas. Our analysis investigates cellular homology, species-specific specializations, and the molecular basis of evolutionary phenotypes across the mammalian brain.
The code is organized into folders corresponding to the major analysis steps and figures in the manuscript:
Scripts for cross-species data integration, quality control, assembly, and reference mapping.
- Cross_Species_Integration: Functions and scripts for integrating human and macaque data.
- QC_and_Assembly: Quality control pipelines and genome assembly annotations.
- Reference_Mapping: Tools for mapping cells between species (e.g., Macaque to Human).
Analysis focusing on the identity and evolutionary specialization of Layer 4 (L4) cortical neurons.
- Species composition analysis.
- L4 marker gene expression (e.g., RORB, FOXP2).
- Differential expression analysis between primates and non-primates.
Construction of the cross-species thalamic atlas and investigation of spatial organization.
- Clustering and annotation of thalamic cell types.
- Identification of Midbrain-derived Inhibitory (MDI) neurons.
- Spatial transcriptomics integration (Human and Mouse).
- Correlation of cellular proportions with phenotypic traits (e.g., visual acuity).
Downstream analysis linking cellular changes to evolutionary phenotypes and genetics.
- Pathway enrichment analysis.
- Gene expression divergence.
- Correlation with brain weight and cortical folding.
If you use this code or data in your research, please cite our paper:
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This project is licensed under the MIT License.